Alignments for a candidate for ilvI in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Marinobacter adhaerens HP15

Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate GFF974 HP15_953 protein containing thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, N-terminal TPP binding region

Query= curated2:O53554
         (515 letters)



>FitnessBrowser__Marino:GFF974
          Length = 552

 Score =  523 bits (1348), Expect = e-153
 Identities = 282/518 (54%), Positives = 356/518 (68%), Gaps = 11/518 (2%)

Query: 2   NGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYARI 61
           NGAQAL+ TLVD GV+VCF+NPGTSEMHFVAALD  P+MR +L LFEGVATGAADGYAR+
Sbjct: 3   NGAQALMKTLVDAGVEVCFSNPGTSEMHFVAALDDEPKMRAVLALFEGVATGAADGYARM 62

Query: 62  AGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAGT 121
           A +PAA LLHLG GLGNGLANLHNAR+ +VP++ +VGDHATYH KYDA L+SDI+ VA  
Sbjct: 63  ADKPAATLLHLGCGLGNGLANLHNARKGKVPVLNIVGDHATYHVKYDAQLQSDIETVARN 122

Query: 122 VS-GWVRRTEAAADVGADAEAAIAASRSG-SQIATLILPADVCWSDGAHAAAGV--PAQA 177
           VS G+VR  ++   +  DA  AIAA+R+   Q+ATLILPADV W +G   +A +  P   
Sbjct: 123 VSPGFVRTAKSTETLCQDAAEAIAAARTAPGQVATLILPADVSWGEGGVPSAPLAPPTPE 182

Query: 178 AAAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERG 237
            A    V  +A  +RSG+   +L+GG + R P + AAA++   +G   L ETFPT +ERG
Sbjct: 183 PADDATVEAIAKAIRSGKKTALLMGGHSLREPSMLAAAKLAAHSGVTLLAETFPTRMERG 242

Query: 238 AGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEP 297
           AG+P +ER+AY AE A  QL  ++ L+L  +++PVSFFAYPG  S LVP  C+VH LA P
Sbjct: 243 AGLPYIERIAYLAELATVQLTDIEQLILVDSKAPVSFFAYPGKKSYLVPDTCQVHTLAAP 302

Query: 298 GGAADALAA---LADEVAPGTVAP-VAGASRPQLPTGDLTSVSAADVVGALLPERAIVVD 353
               D LA+   L D V      P +    RP  P G LT+      VG L+PE AI+VD
Sbjct: 303 D--QDILASLNKLNDAVGASQAQPKLQPEKRPGRPRGKLTAEKVCKAVGELMPENAIIVD 360

Query: 354 ESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYT 413
           E  T  ++L   TAGAP HD +TLTGGAIG G+P AVGAAVA PDRPV+ L  DG+AMYT
Sbjct: 361 EGITSSLMLSVMTAGAPRHDMITLTGGAIGQGLPNAVGAAVACPDRPVIALIGDGTAMYT 420

Query: 414 ISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKI 473
           I  LW+ ARE L+VT++I+NN +Y +L IEL+RVGA  + G KA   LD+  P ++F ++
Sbjct: 421 IQALWTMAREQLNVTSIIFNNASYSVLNIELERVGA-EEAGEKAKSQLDLRGPVINFAEM 479

Query: 474 AEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVVP 511
           A GMGV   RV T EE A AL  A   PGPH+I+ ++P
Sbjct: 480 ANGMGVHGVRVHTAEEMAKALEYAQRMPGPHVIEAMIP 517


Lambda     K      H
   0.318    0.134    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 651
Number of extensions: 19
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 515
Length of database: 552
Length adjustment: 35
Effective length of query: 480
Effective length of database: 517
Effective search space:   248160
Effective search space used:   248160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis